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BIOC 299 > Nucleic Acids, DNA structure, Genome, DNA packaging > Flashcards

Nucleic Acids, DNA structure, Genome, DNA packaging Flashcards

1
Q

What did Friedrich Miescher do?

A

he isolated a molecule, which he called “Nuclein” (DNA) from used bandages

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2
Q

What did Gregor Mendel do?

A

He demonstrated the heritability of genes

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3
Q

What did Miescher determine about the “nuclein” molecule he isolated?

A

it contained a lot of nitrogen and phosphorous

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4
Q

Who first isolated DNA?

A

Friedrich Miescher from used bandages

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5
Q

Who first demonstrated inheritance?

A

Gregor Mendel

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6
Q

Who first discovered chromatin?

A

Walther Flemming

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7
Q

What animal was chromatin first discovered in?

A

Salamanders

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8
Q

What is the primary structure of nucleic acids?

A

the order of the bases in the polynucleotide sequence

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9
Q

What is the secondary structure of nucleic acids?

A

the 3D backbone

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10
Q

What is the tertiary structure of nucleic acids?

A

the supercoiling

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11
Q

What are the 2 main types of nucleic acids?

A

DNA and RNA

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12
Q

What is the major difference between DNA and RNA?

A

they are structurally different in their secondary and tertiary structures

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13
Q

What is the smallest unit of a polymer?

A

a monomer

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14
Q

What are the monomers of nucleic acids?

A

nucleotides

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15
Q

What is an individual nucleotide made of?

A

a nitrogenous base
a sugar
a phosphoric acid residue

all covalently bonded together

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16
Q

What bond connects the 3 components of a nucleotide?

A

covalent bond

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17
Q

T or F: the order of the bases in the nucleic acids of DNA doesn’t matter

A

FALSE! it’s crucial for producing the correct base sequence in the RNA and therefore the correct amino acid sequence for proteins

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18
Q

What are the 2 types of nucleic acid bases?

A

pyrimidines
purines

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19
Q

Describe pyrimidine bases

A

single-ring aromatic compounds

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20
Q

What are the 3 common pyrimidine bases?

A

cytosine (C)
thymine (T)
uracil (U)

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21
Q

Out of the 3 pyrimidine bases, which ones are found in DNA? in RNA?

A

DNA:
cytosine (C)
Thymine (T)

RNA:
Cytosine (C)
Uracil (U)
thymine (T) is in SOME RNA

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22
Q

What are the two common purine bases?

A

adenine (A)
guanine (G)

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23
Q

Which of the 2 purine bases are found in DNA? in RNA?

A

both adenine (A) and guanine (G) are found in both DNA and RNA

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24
Q

Describe purine bases

A

double-ring aromatic compounds

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25
Q

Which of the two major base types consist of single ring aromatics?

A

pyrimidine

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26
Q

Which of the two major base types consist of double ring aromatics?

A

purine

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27
Q

What are the other less common bases referred to as?

A

‘unusual’ bases

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28
Q

What is a nucleoside?

A

a nucleotide without the phosphate residue

a covalently bonded base and sugar

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29
Q

What is the difference between a nucleoSide and a nucleoTide?

A

nucleosides = nitrogenous base + sugar
nucleotides = nitrogenous base + sugar + phosphate residue

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30
Q

What kind of linkage is seen between the sugar and nitrogenous base in a nucleoside?

A

glycosidic linkage

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31
Q

What is a ribonucleoside?

A

a nucleoside (sugar + nitrogenous base) where the sugar is a Beta-D-ribose

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32
Q

What is a deoxyribonucleoside?

A

a nucleoside (sugar + nitrogenous base) where the sugar is a beta-D-deoxyribose

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33
Q

Where does the glycosidic linkage occur in nucleosides with pyrimidine bases? In purine bases?

A

Pyrimidine: between the C-1’ carbon of the sugar to the N-1 nitrogen of the pyrimidine base

purine: between the C-1’ carbon of the sugar and the N-9 nitrogen of purine base

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34
Q

in structural drawings of the nitrogenous bases, which of the molecules has numbered atoms with primes?

A

atoms in the sugar are prime so they don’t get confused when referring to the glycosidic linkage

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35
Q

Where does the phosphate group attach to the nucleoside to make a nucleotide?

A

phosphoric acid is esterified to a hydroxyl group on the sugar

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36
Q

How is a nucleotide named?

A

after the parent nucleoside with a suffix ‘-monophosphate’ and the position of the phosphate ester is numbered after the number of the carbon attached to the hydroxyl group

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37
Q

Which types of nucleotides are most common in nature?

A

5’ nucleotides

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38
Q

What is the difference between a ribose and a deoxyribose?

A

ribose sugars have two hydroxyl groups on the ring (C-2’ and C-3’)

deoxyribose. sugars have only one hydroxyl group on the ring (C-3’)

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39
Q

How are the 4 RNA nucleosides named?

A

Adenosine
Guanosine
Cytidine
Uridine

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40
Q

How are the 4 RNA nucleotides named?

A

Adenosine Monophosphate (AMP)
Guanosine Monophosphate (GMP)
Cytidine Monophosphate (CMP)
Uridine Monophosphate (UMP)

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41
Q

How are the 4 deoxynucleosides named?

A

deoxyadenosine
deoxyguanosine
deoxycytidine
deoxythymidine

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42
Q

How are the 4 deoxynucleotides named?

A

deoxyadenosine monophosphate (dAMP)
deoxyguanosine monophosphate (dGMP)
deoxycytidine monophosphate (dCMP)
deoxythymidine monophosphate (dTMP)

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43
Q

What is formed by the polymerization of nucleotides?

A

nucleic acids

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44
Q

How are nucleotides polymerized?

A

by 3’-5’ phosphodiester bonds (aka, 2 ester bonds formed by phosphoric acid)

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45
Q

Describe a 3’-5’ phosphodiester bond

A

phosphoric acid is esterified to the 3’ hydroxyl group of one nucleotide and the 5’ hydroxyl group of a second nucleotide

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46
Q

How are nucleotide residues in nucleic acids numbered?

A

from 5’-3’

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47
Q

What does the 5’ end of a nucleic acid usually have?

A

a phosphate group

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48
Q

What does the 3’ end of a nucleic acid usually have?

A

a free hydroxyl group

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49
Q

What is the most important component of nucleic acids?

A

the nitrogenous bases, the order of these is important (ACGT does not equal TGCA)

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50
Q

t or f: the DNA chain has polarity

A

true

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51
Q

What does it mean for the DNA chain to be polar?

A

that there are two distinct ends, the 5’ end is different from the 3’ end

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52
Q

In what direction do we ALWAYS read the nitrogenous base pair order?

A

from 5’ –> 3’

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53
Q

What were the 3 key experiments for studying DNA?

A

Griffith
Avery, Macleod, McCarty
Hershey and Chase

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54
Q

Describe Griffith’s Transforming Principle Experiment

A

exp 1:
he used two types of Streptococcus pneumoniae bacteria: smooth virulent and rough non-virulent
- smooth virulent = killed mice
- rough nonvirulent = mice lived

exp 2:
heat treated and killed the smooth virulent bacteria = mice lived

exp 3:
combined heat-killed smooth virulent bacteria and live rough nonvirulent bacteria = mice killed

results:
- collected the colonies and found they were all smooth virulent bacteria
- nonvirulent bacteria were able to transform the molecule of inheritance (unknown that it was DNA) from the heat-killed virulent cells and become virulent

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55
Q

Describe the Avery, MacLeod and McCarty transforming principle identification experiment

A

they did studies in which they tested an extract of the heat-killed smooth bacteria:

  1. removing lipids and proteins = bacteria active (mice died)
  2. added proteases = bacteria active (mice died)
  3. added ribonucleases = bacteria active (mice died)
  4. added deoxyribonuclease = bacteria INACTIVE (mice lived)

results: the only thing that causes the bacteria to be ineffective was the deoxyribonuclease which breaks down DNA = evidence that DNA is the transforming principle (molecule of inheritance)

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56
Q

Describe the Hershey and Chase blender experiment

A

used bacteriophage (protein and DNA, infect bacteria)

  1. radioactively labelled bacteriophage DNA
  2. radioactively labelled bacteriophage protein coating

bacteriophage allowed to enter bacteria
blended to remove phage

results:
the radioactive protein coating on the phage was shed outside of the bacteria and not found inside the bacterial cell = the transformation principle cannot be protein

the radioactively labelled DNA was found inside the bacterial cell = must be the molecule of inheritance

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57
Q

Whose data about the Xray diffraction patterns of DNA and the double helix structure were ripped off?

A

Rosalind Franklin likely first discovered DNA is most likely a double helix

her data was ripped off by Watson and Crick and was not referenced

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58
Q

How was the double-helical structure of DNA determined?

A

by building models based on X-ray diffraction patterns by Rosalind Franklin and Maurice Wilkins

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59
Q

What did the X-ray diffractions and model building suggest about the components of DNA?

A

that the amount of Adenine (A) always equalled the amount of Thymine (T)
and the amount of Guanine (G) always equalled the amount of Cytosine (C)

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60
Q

What is Chargaff’s rule?

A

that in DNA, the amount of A always = T, and amount of G always = C

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61
Q

What did Chargaff’s rule and Franklin and Wilkin’s data suggest?

A

that DNA is made of two polynucleotide chains wrapping around one another to make a helix

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62
Q

What bonds the base pairs of the two strands in DNA?

A

hydrogen bonds

63
Q

T or F: the two strands of DNA run parallel to one another

A

false!! they run antiparallel: 5’-3’ and one 3’-5’

64
Q

What does complementary mean?

A

refers to the base pairing between:
A-T
G-C
this occurs along the entire strands

so the strands are complementary

65
Q

How many hydrogen bonds occur between A-T?

A

two hydrogen bonds

66
Q

How many hydrogen bonds occur between G-C?

A

three hydrogen bonds

67
Q

What are the grooves of a DNA double helix?

A

there are two grooves: major (larger) and minor (smaller)

occurs because the atoms in the two strands don’t completely fill the helix

68
Q

What function do the two grooves in the double helix structure of DNA serve?

A

they are sites for polypeptides to bind

69
Q

T or F: the sugar-phosphate backbone of DNA is negatively charged

A

true because of all the phosphate groups which are negatively charged

70
Q

What neutralizes the negative charge of the sugar-phosphate backbone?

A

positively charged ions (Na+ or Mg2+) and polypeptides with + side chains bond with the backbone (ex. histones)

71
Q

What are the 3 forms of DNA?

A

A-DNA
B-DNA
Z-DNA

72
Q

Which is the most commonly occurring form of DNA?

A

B-DNA

73
Q

How many base pairs does one complete turn of the helix in a B-DNA molecule have?

A

10 base pairs

74
Q

How many base pairs does one complete turn of the helix in a A-DNA molecule have?

A

11 base pairs

75
Q

Which conformation of DNA is most common (left or right)?

A

right

76
Q

T or F: the A-DNA is a left-handed helix whereas, the B-DNA is right-handed

A

false, both are right-handed

77
Q

How can you determine a right-handed helix vs a left?

A

curl fingers of your right hand with thumb pointing up

the helix winds UPwards in the direction the fingers curl

78
Q

Describe Z-DNA. When does it occur?

A

left-handed DNA
occurs usually when there’s alternating purine-pyrimidine sequences (ex. CGCGCG)

one side of the backbone is flipped 180 degrees and looks more zigzagged

79
Q

What is base stacking?

A

a process in which the hydrophobic ring portions of the DNA bases interact via VDW interactions

80
Q

What is Canonical base pairing (or Watson/Crick type)?

A

where A-T and G-C

81
Q

What does the extra hydrogen bond in the G-C bond provide?

A

extra stability

82
Q

What forces are working to stabilizes the double helix?

A

hydrophobic effects

stacking interactions / base stacking (VDW) (between hydrophobic rings)

hydrogen bonds (holding strands together)

charge-charge interactions (phosphodiester backbone is -)

83
Q

What is the purpose of the major and minor grooves?

A

openings in the helix allow for hydrogen-binding of the exposed base pairs

allows DNA to interact with other molecules during replication and transcription

84
Q

Who almost solved the structure of DNA 20 years before everyone else? what did they find?

A

Florence Bell and William Astbury

found that base pairs are stacked

85
Q

When is the form of DNA and the grooves most obvious?

A

when DNA is dehydrated

86
Q

When looking at the structures of A- and B-DNA what is the major difference?

A

the grooves in the A-DNA are all similar width, whereas in B-DNA, there’s the minor and major grooves of different widths

87
Q

What needs to be done to the DNA in order to study the genetic information?

A

it needs to be denatured

88
Q

What does DNA denaturation mean?

A

the double helix is unfolded into two single strands

89
Q

How can DNA be denatured?

A

either experimentally using heat or enzymes
or biologically using enzymes

90
Q

T or F: once denatured, DNA cannot be renatured/reannealed back to its original state

A

false, it can be renatured

91
Q

How is DNA heat denaturation monitored?

A

by observing the ultraviolet light absorption of the nitrogenous bases

92
Q

When DNA is denatured with heat, how is UV light absorption used to monitor the melting?

A

nitrogenous bases absorb light at 260nm wavelength (UV)

as denaturation occurs, the strands separate, and the amount of light absorbed increases

93
Q

What is native DNA?

A

DNA in the double helix form (compared to denatured DNA)

94
Q

What is hyperchromicity?

A

the increase of light absorption that occurs when DNA is exposed to heat and the strands are pulled apart

95
Q

Why does hyperchromicity (increased light absorption during DNA heat denaturation) occur?

A

because the bases are stacked in native DNA, but unstacked when DNA is denatured = more light can be absorbed

96
Q

Why does breaking apart G-C base pairs require more energy to denature than A-T?

A

because G-C bases have 3 hydrogen bonds as opposed to 2 in A-T

97
Q

What does the inflection point/halfway point signify in a DNA heat denaturation curve?

A

the melting point temperature

98
Q

DNA that consists of more G-C base pairs will have a higher or lower Tm (melting point) than that of DNA which consists of more A-T base pairs? why?

A

HIGHER Tm in G-C because these pairs have 3 Hbonds, require more energy to break

99
Q

How can DNA be renatured? what factor can cause improper base pairing?

A

by cooling the separated strands to 20-25 degrees below Tm

rapid cooling to a much lower temperature than Tm can cause improper base pairing - this can be fixed by warming to 20-25 below Tm

100
Q

What purpose do DNA microarrays (chips) and qPCR (quantitative polymerase chain reaction) have?

A

they can be used to identify mutations in genes and used to identify gene expression

also have biomedical influences such as in diagnostics/prognostics, therapy, and biological predispositions

101
Q

What is the genome?

A

all genetic material (DNA) in a cell - ie., all the base pairs

the genome contains the genes that code for (are transcribed and translated into) proteins that are made in an organism

102
Q

What is a transcriptome?

A

all the RNA in a cell

103
Q

What is a proteome?

A

all the protein in a cell

104
Q

What is the linear path/central dogma of DNA?

A

DNA replication
DNA transcription to make RNA
RNA translation to make proteins

105
Q

T or F: the path from DNA to protein is linear and cannot be reversed except in some viruses

A

true, but only transcription can be reversed in specific viruses, once RNA has been translated, it cannot be reversed

106
Q

How much of the human genome is coding genes?

A

~2%

107
Q

T or F: all species have the same sized genomes

A

false - huuuuge range of sizes

108
Q

T or F: generally, more genes (larger genome) = more complex organism

A

true, but there’s a lot of exceptions

109
Q

Describe the Human Genome Project

A

cost $3 billion

goals:
1. sequence one entire human genome (3 billion base pairs)
2. identify all genes and functions
3. to be used for understanding mutations that cause disease

begun in 1990, completed in 2022

110
Q

How big is the human genome?

A

there’s 3 billion base pairs

111
Q

Now that genome sequencing has significantly improved, how much faster/cheaper is it to sequence the human genome?

A

Significantly

the HGP took 30 years and $3 billion to sequence one genome, now costs $600/genome and takes a few hours/days

112
Q

How long is the human genome (DNA)? How big is the nucleus it’s packed into?

A

2 meters of DNA packed into a nucleus with the diameter of ~0.2-2 micrometers

113
Q

How long is the bacterial genome (DNA)? how big is the cell it’s packed into?

A

~1.6 mm of DNA packed into a cell that’s ~2 micrometers long

114
Q

How is DNA compacted and packed into cells or the nucleus of cells?

A

supercoiling

115
Q

What features of bacterial DNA packaging are different from eukaryotic DNA?

A
  1. histone-like proteins, but no true histones
  2. no nucleosome-like particles
  3. DNA not associated with proteins
  4. supercoiled nucleoid structure = DNA attached to scaffold in large loops (~100 kb)
116
Q

What shape is bacterial DNA?

A

circular

117
Q

If bacterial DNA strands are under-wound, they form what type of supercoils?

A

negative - with fewer turns

118
Q

If bacterial DNA strands are over-wound, they form what type of supercoils?

A

positive - with more turns

119
Q

What type of supercoiling does naturally occurring bacterial (circular) DNA have?

A

negative supercoiling except during replication where it’s positively supercoiled

120
Q

What mediates the negative and positive supercoiling of bacterial DNA?

A

enzymes called topisomerases

121
Q

What are the 2 classes of topisomerases? what do they each do?

A

Class I: cleave the backbone of one DNA strand, pass the other end through and reseal = removes supercoils

Class II: cleave the backbone of both DNA strands, pass either end through, and reseal = adds supercoils

122
Q

What is an example of how supercoiling can be controlled biomedically?

A

antibiotics can interrupt coiling in bacteria to prevent diseases such as UTIs

123
Q

What is a major feature of eukaryotic nuclear DNA that is lacking in bacterial DNA? and makes eukaryotic DNA much more complex?

A

chromatin

124
Q

What is chromatin?

A

eukaryotic DNA has chromatin, which is what chromosomes are composed of

chromatin consists of proteins, DNA, and RNA

125
Q

What is the major component of chromatin?

A

histone proteins

126
Q

How is chromatin made?

A

electrostatic interactions occurring between the negatively charged phosphate groups and the basic proteins with positively charged side chains (at physio pH) of DNA create a complex

127
Q

What is eukaryotic DNA packaged in?

A

chromatin

128
Q

What is the function of chromatin?

A

to package DNA into a more compact form

129
Q

What is the fundamental unit of chromatin?

A

nucleosome

130
Q

Describe nucleosomes

A

the first level of eukaryotic DNA packaging/ DNA folding

131
Q

What is the first level of eukaryotic DNA packaging/folding?

A

beads on a string

nucleosomes (beads) = DNA wrapped around a histone protein core attached by ‘spacer regions’

string = spacer regions = DNA and some H1 and other proteins

132
Q

what are the 5 types of histone proteins found in chromatin?

A

H1, H2A, H2B, H3, H4

133
Q

What amino acids are the main components of histone proteins in chromatin?

A

basic (+ charged) AAs like lysine and arginine

134
Q

In chromatin, which type of histone is the DNA tightly bound to? which is not tightly bound to?

A

DNA is tightly bound to H2A, H2B, H3, H4
DNA is not tightly bound to H1

135
Q

What is the composition of each nucleosome?

A

1 H1 molecule
2x H2A, H2B, H3, H4 molecules (octamer)
~200 bp of DNA

136
Q

Why does the octamer of histones bind so tightly to the DNA in the beads and string structure to form nucleosomes?

A

because the histones in the octamer (H2A, H2B, H3, H4) are composed of positively charged amino acids (lysine, arginine) which interact with the negatively charged phosphate groups of the sugar-phosphate backbone of DNA

137
Q

How many base pairs are in one nucleosome?

A

~200

138
Q

What is the significance of the amino acid tails projecting out of the octamer of chromatin?

A

it means they can be post-translationally modified

139
Q

What is the octamer of chromatin?

A

2 molecules of H2A, H2B, H3, H4 histone proteins

140
Q

what’s the core particle?

A

the histone octamer and 146 bp of DNA

141
Q

What’s the nucleosome?

A

the core particle (histone octamer + 146 bp) + 54 bp + histone H1

142
Q

How many molecules of H1 are there per nucleosome?

A

1

143
Q

What is the second stage of eukaryotic DNA packaging? how much compaction is there?

A

chromatin scaffolds

10000x compaction

144
Q

What is the result of chromatin scaffolds?

A

chromosomes that are 1 micrometer in diameter and 5-10 micrometers long

145
Q

How much compaction is there in B-DNA?

A

1x compaction

146
Q

How much compaction is there in nucleosomes?

A

7x

147
Q

How much compaction is there in chromatin fiber?

A

~50x

148
Q

How much compaction is there in chromatin scaffolds?

A

~10,000x

149
Q

What are epigenetics?

A

when gene activity is regulated by something (e.g., environmental factor) that is NOT actually changing DNA and IS heritable

150
Q

T or F: epigenetics are changes to the DNA

A

false!! no changes to the DNA, just a change to regulation of gene activity

151
Q

T or F: epigenetics are heritable

A

true

152
Q

What is an example of epigenetics?

A

Agouti mice

153
Q

What kind of DNA code doe epigenetics involve?

A

one with

modified base pairs (ex. methyl-cytosine)
chemically-modified N-terminal histone tails (amino acids can be phosphorylated, methylated, or acetylated)

153
Q

What kind of DNA code doe epigenetics involve?

A

one with

modified base pairs (ex. methyl-cytosine)
chemically-modified N-terminal histone tails (amino acids can be phosphorylated, methylated, or acetylated)

BIOC 299 (16 decks)

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